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Package `RSAGA`

1. Inf cbind TRUE range radius na strings NA pick from saga grid data filename path varname prec 7 show output on console FALSE env rsaga env Arguments data data frame giving the coordinates in columns specified by X name Y name of point locations at which to interpolate the specified variables or grid values src shapefile data frame or point shapefile pick variables to be picked interpolated from src if missing use all available variables except those specified by X name and Y name method interpolation method to be used uses a partial match to the alternatives nearest neighbor currently the default and krige set na logical if a column with a name specified in pick already exists in data how should it be dealt with set na FALSE default only overwrites existing data if the interpolator yields a non NA result set na TRUE passes NA values returned by the interpolator on to the results data frame radius numeric value specifying the radius of the local neighborhood to be used for interpolation defaults to 200 map units presumably meters or in the functions for grid files 2 5 cellsize nmin nmax numeric for method krige only see krige function in package gstat 18 sill range nugget model log pick from points numeric for method krige only the overall sill parameter to be used for the variogram numeric for method krige only the var
2. 7 northwest If minslope 0 depressions will only be filled until a horizontal surface is established which may not be helpful for hydrological modeling Author s Alexander Brenning R interface Volker Wichmann SAGA module References Planchon O and F Darboux 2001 A fast simple and versatile algorithm to fill the depressions of digital elevation models Catena 46 159 176 rsaga filter gauss 33 Wang L amp H Liu 2006 An efficient method for identifying and filling surface depressions in digital elevation models for hydrologic analysis and modelling International Journal of Geograph ical Information Science Vol 20 No 2 193 213 See Also rsaga sink removal rsaga sink route rsaga filter gauss Gauss Filter Description Smooth a grid using a Gauss filter Usage rsaga filter gauss in grid out grid sigma radius ceiling 2 sigma Arguments in grid input SAGA grid file default file extension sgrd out grid output SAGA grid file sigma numeric 20 0001 standard deviation parameter of Gauss filter radius positive integer radius of moving window optional arguments to be passed to rsaga geoprocessor including the env RSAGA geoprocessing environment Value The type of object returned depends on the intern argument passed to the rsaga geoprocessor For intern FALSE itis a numerical error code 0 success or otherwise default a character vector with the module s console ou
3. rsaga hillshade and other higher level functions rsaga get modules 37 Examples Not run rsaga hillshade dem hillshade exaggeration 2 using the RSAGA geoprocessor rsaga geoprocessor ta lighting 0 1list E equivalent DOS command line call saga cmd exe ta lighting 0 silent ELEVATION dem sgrd SHADE hillshade EXAGGERATION 2 H EVATION dem sgrd SHADE hillshade EXAGGERATION End Not run rsaga get modules Find SAGA libraries and modules Description These functions list the SAGA libraries rsaga get libraries and modules rsaga get lib modules rsaga get modules available in a SAGA installation and allow to perform a full text search among these functions Usage rsaga get libraries path rsaga env S modules dll Platform dynlib ext rsaga get lib modules lib env rsaga env interactive FALSE rsaga get modules libs env rsaga env rsaga search modules text modules search libs TRUE search modules TRUE env rsaga env ignore case TRUE Arguments text character string to be searched for in the names of available libraries and or modules search libs search modules logical default TRUE should text be searched for in library and or module names ignore case logical default FALSE should the text search in library module names be case sensitive lib libs character vector 1
4. ties method see rank Value If x is provided a numeric value in the interval 0 1 is returned If x is missing a character vector of same length giving suggested variable or file names here relpos and relrank respectively See focal function for details Author s Alexander Brenning See Also focal function rank centervalue Examples m matrix round runif 9 1 10 ncol 3 print m relative position m relative rank m Not run focal function dem fun relative rank radius 5 focal function dem fun relative position radius 5 relrank as vector read ascii grid relrank data relpos as vector read ascii grid relpos Sdata resid median 23 plot relpos relrank pch cor relpos relrank use complete obs method pearson End Not run resid median Residual Median and Quantile Filters for Grids Description These functions use the median and other quantiles to describe the difference between a grid value and its neighborhood They are designed for use with focal function Usage resid median x resid minmedmax x resid quartiles x resid quantile x probs Arguments x a Square matrix with the grid data from the moving window possibly containing NA values probs numeric vector of probabilities in 0 1 to be passed to quantile Details These functions are designed for being called by focal function which repeatedly passes the
5. 2004 Spatial variability of snow accumulation on Vernagt ferner Austrian Alps in winter 2003 2004 Zeitschrift fuer Gletscherkunde und Glazialgeologie 39 43 57 Winstral A Elder K Davis R E 2002 Spatial snow modeling of wind redistributed snow using terrain based parameters Journal of Hydrometeorology 3 524 538 See Also focal function quantile Examples Settings used by Plattner et al 2004 ctrl wind shelter prep 6 pi 4 pi 12 10 Not run focal function dem asc fun wind shelter control ctrl radius 6 search mode circle End Not run Index Topic file read ascii grid 19 RSAGA package 2 Topic spatial rsaga esri to sgrd 27 rsaga import gdal 44 rsaga sgrd to esri 56 set file extension 64 Topic interface read ascii grid 19 RSAGA package 2 rsaga add grid values to points 23 rsaga close gaps 24 rsaga contour 25 rsaga env 26 rsaga esri to sgrd 27 rsaga esri wrapper 28 rsaga fill sinks 30 rsaga filter gauss 32 rsaga filter simple 33 rsaga geoprocessor 34 rsaga get modules 36 rsaga get usage 38 rsaga grid calculus 39 rsaga grid to points 4l rsaga hillshade 42 rsaga html help 43 rsaga import gdal 44 rsaga insolation 46 rsaga inverse distance 48 rsaga local morphometry 50 rsaga ordinary kriging 52 rsaga parallel processing 54 rsaga sgrd to esri 56 rsaga sink removal 57 rsaga sink route 58 rsaga solar radiation 59 rsaga target 61 rsag
6. Also focal function grid predict 10 grid to xyz Examples Not run Assume that d is a data frame with point observations of a numerical response variable y and predictor variables a b and c Fit a generalized additive model to y a b c We want to model b and c as nonlinear terms require gam fit gam y a s b s c data d multi focal function in grids c a p c out varnames pred fun grid predict fit fit Note that the grid predict uses by default the predict method of fit Model predictions are written to a file named pred asc End Not run Not run A fake example of a logistic additive model require gam fit gam cl a s b s c data d family binomial multi focal function in grids c a p c out varnames pred fun grid predict fit fit control predict list type response control predict is passed on to grid predict which dumps its contents into the arguments for fit s predict method Model predictions are written to a file named pred asc End Not run grid to xyz Convert Grid Matrix to x y z data frame Description Convert a grid matrix to a x y z data frame Usage grid to xyz data header varname z colnames c x y varname Arguments data grid data either a grid data matrix or a list with components data a matrix with the grid data and header
7. GIS ver sion try one of these two options or look at rsaga get usage and use rsaga geoprocessor directly sorry for the inconvenience numeric coefficient vector to be used for the linear combination of the in grids If coef as one more element than in grids the first one will be interpreted as an intercept integer number of digits used when converting the coefficients to character strings trailing zeros will be removed logical if TRUE terms grids with coefficient numerically equal to zero after rounding to c digits digits will be removed from the formula logical if TRUE default factors equal to 1 after rounding to c digits digits will be removed from the formula optional arguments to be passed to rsaga geoprocessor including the env RSAGA geoprocessing environment rsaga grid calculus 41 Details The in grids are represented in the formula by the letters a for in grids 1 b etc Thus if in grids 1 is Landsat TM channel 3 and in grids 2 is channel 4 the NDVI formula TM3 TM4 TM3 TM4 can be represented by the character string a b a b any spaces are removed or the formula a b a b in the formula argument In addition to and the following operators and functions are available for the formula definition power sin a sine cos a cosine tan a tangent asin a arc sine acos a arc cosine atan a arc tangent atan2 a b arc tangent of b a abs a absolute value int
8. a Y AR REN 25 ISsaga CODLOUR is Ee ee oe AS Ee qued revu dite x Wege dos 26 A uode dosis up god uote n Wege diio tras e ee dudit URP n 27 ISApa eSELIOJSPET ia n Sx Go e Rb Se S 28 rsaga esri WrapDer so s aoeeoe e eoa kook o e ea a a E a a E E S 29 rsaga fl sinks 25d ke a ek tok E Pos E vero E moon E 31 Isapa hltergausS 239 oe ck AE ROG eh EE s AG Rk Sk GS RR e tian 33 rsaga filtersumple o e eoc s e oe b yo o n Rom X oh ho Pom RR e ee 34 rsaga geoprocessOr onoo 35 rsaga pet Modules e 6 spe so ego e E e S Y ORUORIE RR 3 39 Tsapa petuUsage ue Mie SENG Ss A Ss que Ro qe e dors 39 rsaga prid calculus sop sia n EX RUE OR ape E n 40 rsaga grid to points lehren 42 rsaga hillshade e sudo OR ERR UR OER ESR ERY Oh UR Rs 43 rsaga html help s saai inse eS A OY ROO UV VOX e o ROS OR s 44 rsapaimportgdal s i 2 2 nk A RE RR m m A Rm 45 rsaga insOlatiOD ooo ss s o e ono boe koe 9 oe EORR X CR o Pom RU e ee 47 rsagainverse distance LL 49 rsaga localmorphometry 2r 31 rsaga ordinary kriging LL 53 rsaga parallel processing e 23 Tsapa sprdtoOcestl oso Seng Soho n d Y E e ine 57 rsapa sink femoval ii s kv EORR eR A EES URS E OR 3 58 TSApa SIDK FOULE 0 si ce vr Sue Eee BRR ee deeds 59 rsapa solarradiatiOn gt s 2 s e RR RR e RE EI E Pc x Ps 60 tsaga target ono loose e wok SDN E ae ee E b Ron E 62 rsaga wetness index LL 63 setfile eXt nSIOD o o soo Por Xo Ro OD m Oe ve wo UR OP ROW m od y eR UR RN Ld 65 wind shelter s oo
9. a convert to integer sqrt a square root In a natural logarithm mod a b modulo gt a b returns 1 if a greater b It a b returns 1 if a lower b eq a b returns 1 if a equal b ifelse switch x y returns x if switch equals 1 else y Using remove zeros FALSE might have the side effect that no data areas in the grid with coefficient 0 are passed on to the results grid To be confirmed Value The type of object returned depends on the intern argument passed to the rsaga geoprocessor For intern FALSE itis a numerical error code 0 success or otherwise default a character vector with the module s console output Note This function uses module 1 in the SAGA library grid calculus Author s Alexander Brenning R interface Olaf Conrad SAGA module 42 rsaga grid to points See Also local function focal function and multi focal function for a more flexible framework for combining grids or applying local and focal functions xsaga geoprocessor rsaga env Examples Not run using SAGA grids calculate the NDVI from Landsat TM bands 3 and 4 rsaga grid calculus c tm3 sgrd tm4 sgrd ndvi sgrd a b a b apply a linear regression equation to grids coefs c 20 0 6 maybe from a linear regression of mean annual air temperature MAAT against elevation something like coefs coef lm maat elevation rsaga linear combination elevation sgrd maat sgrd coefs equivalent rsaga grid
10. arg pmatch Examples Based on example from match arg require stats center lt function x type c mean median trimmed multi focal function 13 type lt match arg ext type base 0 switch type mean mean x median median x trimmed mean x trim 1 x rcauchy 10 center x t Works center x 2 Same for base 0 center x med Works center x 1 Same for base 0 try center x m Error multi focal function Focal Grid Function with Multiple Grids as Inputs Description multi focal function cuts out square or circular moving windows from a stack of grids matrices and applies a user defined matrix function that takes multiple arguments to this data This is especially useful for applying predict methods of statistical models to a stack of grids containing the explanatory variables see Examples and grid predict The function is suitable for large grid files as it can process them row by row but it may be slow because one call to the focal function is generated for each grid cell Usage multi focal function in grids in grid prefix in factor grid out grid prefix path NULL in path path out path path fun in varnames out varnames radius 0 is pixel radius TRUE na strings NA valid ranges nodata values c out nodata value search mode c circle square digits 4 dec quiet TRUE nlines In
11. it model Details grid predict is a simple wrapper function First it binds the arguments in together ina data frame with the raw predictor variables that have been read from their grids by the caller multi focal function Then it calls the optional trafo function to transform or combine predictor variables e g perform log transformations ratioing arithmetic operations such as cal culating the NDVI Finally the predfun or typically the default predict method of fit is called handing over the fit the predictor data frame and the optional cont rol predict arguments Value grid predict returns the result of the call to predfun or the default predict method Note Though grid predict canin principle deal with predict methods returning factor variables its usual caller multi focal function cannot classification models should be dealt with by setting at ype prob for rpart or type response for logistic regression and logistic additive model argument for example see second Example below Author s Alexander Brenning References Brenning A 2008 Statistical geocomputing combining R and SAGA The example of land slide susceptibility analysis with generalized additive models In J Boehner T Blaschke L Montanarella eds SAGA Seconds Out Hamburger Beitraege zur Physischen Geographie und Landschaftsoekologie 19 23 32 http www environment uwaterloo ca u brenning Brenning 2008 RSAGA pdf See
12. otherwise default a character vector with the module s console output Author s Alexander Brenning R interface Olaf Conrad SAGA module See Also rsaga geoprocessor rsaga env 27 rsaga env Set up the RSAGA Geoprocessing Environment Description rsaga env creates a list with system dependent information on SAGA path module path and data working directory Such a list is required by all RSAGA geoprocessing functions Usage rsaga env workspace cmd ifelse Platform OS type windows saga cmd exe saga cmd path modules check libpath TRUE check SAGA TRUE check PATH Platform OS type windows check os default TRUE os default path ifelse PlatformSOS type windows C Progra 1 SAGA GIS usr local bin Arguments workspace path of the working directory for SAGA defaults to the current directory cmd name of the SAGA command line program defaults to saga_cmd exe its name under Windows path path in which to find cmd rsaga env is usually able to find SAGA on your system if it is installed see Details modules path in which to find SAGA libraries see Details check libpath if TRUE default first look for SAGA in the folder where the RSAGA package is installed check SAGA if TRUE default next check the path given by the environment variable SAGA if it exists check PATH if TRUE default on Windows next look for SAGA in all the paths
13. prediction is desired predfun optional prediction function if missing the fit s predict method is called In some cases it may be convenient to define a wrapper function for the predict method that may be passed as predfun argument trafo an optional function x thattakesa data frame x and returns a data frame with the same number of rows this is intended to perform transformations on the input variables e g derive a log transformed variable from the raw in put read from the grids or more complex variables such as the NDVI etc the data frame resulting from a call to trafo if provided is passed to predfun control predict an optional list of arguments to be passed on to predfun this may be e g type response to obtain probability prediction maps from a logistic re gression model grid predict 9 predict column optional character string Some predict methods e g predict 1da return a data frame with several columns e g one column per class in a classification problem predict column is used to pick the one that is of interest trace integer gt 0 positive values give more 2 or less 1 information on predictor variables and predictions location optional location data received from multi focal function is added to the newdata object that is passed on to predfun these arguments are provided by the calling function usually multi focal function They contain the explanatory predictor variables required by the
14. rsaga wetness index dem sgrd swi sgrd End Not run set file extension Determine or modify file name extensions Description Function get ile extensiondetermines the file extension set file extension changes it and default file extension changes it only if it is not already specified Usage set file extension filename extension fsep Platform file sep get file extension filename fsep Platform file sep default file extension filename extension force FALSI Arguments filename character vector file name s possibly including paths and extensions a file name ending with a is interpreted as having extension while a file name that doesn t contain a is interpreted has having no extension extension character string file extension without the dot fsep character separator between paths force logical argument to default file extension force the file extension to be extension same result as set file extension or only set it to extension if it has not been specified Value character vector of same length as ilename Author s Alexander Brenning Examples fnm c C TEMP DIR temp C TEMP DIR tmp txt tempfile get file extension fnm set file extension fnm extension TMP default file extension fnm extension TMP 66 wind shelter wind shelter Wind Shelter Index Description wind shelter is a function to be used with ocal function
15. s Alexander Brenning Examples Not run Check the default RSAGA environment on your computer rsaga env SAGA data in C sagadata binaries in C SAGA GIS myenv rsaga env workspace C sagadata path C SAGA GIS Use the myenv environment for SAGA geoprocessing rsaga hillshade dem hillshade env myenv Creates or overwrites grid C sagadata hillshade sgrd derived from digital elevation model C sagadata dem sgrd End Not run rsaga esri to sgrd Convert ESRI ASCII binary grids to SAGA grids Description rsaga esri to sgrd converts grid files from ESRI s ASCII asc and binary flt format to SAGA s version 2 grid format sgrd Usage rsaga esri to sgrd in grids out sgrds set file extension in grids sgrd in path rsaga esri wrapper 29 Arguments in grids character vector of ESRI ASCII binary grid files default file extension asc files should be located in folder in path out sgrds character vector of output SAGA grid files defaults to in grids with file extension being replaced by sgrd which is also the default extension if file names without extension are specified files will be placed in the current SAGA workspace default rsaga env workspace or env workspace if an env argument is provided in path folder with in grids optional arguments to be passed to rsaga geoprocessor including the env RSAGA geoprocessing environment Value The ty
16. shelter create variable name Examples Not run A simple median filter applied to dem asc gapply dem median radius 3 Same focal function dem fun median radius 3 mw to vector TRUE mw na rm TRUE See how the filter has changed the elevation data dl as vector read ascii grid dem Sdata d2 as vector read ascii grid median data hist dl d2 br 50 8 grid predict End Not run Wind shelter index used by Plattner et al 2004 Not run ctrl wind shelter prep 6 pi 4 pi 12 10 focal function dem fun wind shelter control ctrl radius 6 search mode circle End Not run Or how about this if aspect is local terrain exposur Not run gapply aspect cos how northerly exposed is a pixel gapply aspect sin how easterly exposed is a pixel Same result but faster focal function aspect fun function x c cos x sin x varnames c cos sin End Not run grid predict Helper function for applying predict methods to stacks of grids Description This function can be used to apply the predict method of hopefully any fitted predictive model pixel by pixel to a stack of grids representing the explanatory variables It is intended to be called primarily by multi focal function Usage grid predict fit predfun trafo control predict predict column trace 0 location Arguments fit a model object for which
17. sop ch RS RO AR opt eG BR ARA ata 66 Index 68 RSAGA package RSAGA SAGA Geoprocessing and Terrain Analysis in R Description RSAGA provides access to geocomputing and terrain analysis functions of SAGA from within R by running the command line version of SAGA In addition several R functions for handling and manipulating ASCII grids are provided including a flexible framework for applying local functions including predict methods of fitted models or focal functions to multiple grids Details centervalue 3 Package RSAGA Type Package Version 0 91 1 Date 2010 08 25 License GPL 2 RSAGA provides direct access to SAGA functions including a comprehensive set of terrain analysis algorithms for calculating local morphometric properties slope aspect curvature hydrographic characteristics size height and aspect of catchment areas and other process related terrain at tributes potential incoming solar radiation topographic wetness index and more In addition R SAGA provides functions for importing and exporting different grid file formats and tools for preprocessing grids e g closing gaps or filling sinks RSAGA adds a framework for creating custom defined focal functions e g specialized filter and terrain attributes such as the topographic wind shelter index within R This framework can be used to apply predict methods of fitted statistical models to stacks of grids representing predictor variables Furthermore function
18. to calculate a topographic wind shelter index from a digital elevation model which is a proxy for snow accumulation on the lee side of topographic obstacles wind shelter prep performs some preparatory calculations to speed up repeated calls to wind shelter Usage wind shelter x prob NULL control wind shelter prep radius direction tolerance cellsize 90 Arguments x square matrix of elevation data prob numeric quantile of slope values to be used in computing the wind shelter index if NULL use max equivalent to prob 1 control required argument the result of a call to wind shelter prep radius radius gt 1 of circle segment to be used number of grid cells not necessarily an integer direction wind direction direction from which the wind originates North 0 2 pi clockwise angles tolerance directional tolerance cellsize grid cellsize Details wind shelter implements a wind shelter index used by Plattner et al 2004 for modeling snow accumulation patterns on a glacier in the Austrian Alps It is a modified version of the algorithm of Winstral et al 2002 The wind shelter index of Plattner et al 2004 is defined as Shelter index S arctan max z x0 z x x0 x x in S where S S x0 a da d is the set of grid nodes within a distance lt d from x0 only consid ering grid nodes in directions between a da and a da from x0 The present implementation generalizes this inde
19. under shoots in the surfaces used to fill interpolate the gaps Value The type of object returned depends on the intern argument passed to the rsaga geoprocessor For intern FALSE itis a numerical error code 0 success or otherwise default a character vector with the module s console output Note This function uses modules 7 rsaga close gaps and6 rsaga close one cell gaps from the SAGA library grid tools Author s Alexander Brenning R interface Olaf Conrad SAGA module See Also rsaga geoprocessor rsaga env 26 rsaga contour Examples Not run using SAGA grids rsaga close gaps rawdem sgrd dem sgrd using ASCII grids rsaga esri wrapper rsaga close gaps in dem rawdem out dem dem End Not run rsaga contour Contour Lines from a Grid Description Creates a contour lines shapefile from a grid file in SAGA grid format Usage rsaga contour in grid out shapefile zstep zmin zmax Arguments in grid input digital elevation model DEM as SAGA grid file default file extension sgrd out shapefile output contour line shapefile Existing files will be overwritten zstep zmin zmax lower limit upper limit and equidistance of contour lines arguments to be passed to rsaga geoprocessor Value The type of object returned depends on the int ern argument passed to the rsaga geoprocessor For intern FALSE it is a numerical error code 0 success or
20. undocumented optional arguments to be passed to rsaga geoprocessor including the env RSAGA geoprocessing environment Details The SAGA Wetness Index is similar to the Topographic Wetness Index TWI but it is based on a modified catchment area calculation out mod carea which does not treat the flow as a thin film as done in the calculation of catchment areas in conventional algorithms As a result the SWI tends to assign a more realistic higher potential soil wetness than the TWI to grid cells situated in valley floors with a small vertical distance to a channel Value The type of object returned depends on the intern argument passed to the rsaga geoprocessor For intern FALSE itis a numerical error code 0 success or otherwise default a character vector with the module s console output Note This function uses module 15 from the SAGA library ta hydrology Author s Alexander Brenning R interface Juergen Boehner and Olaf Conrad SAGA module References Boehner J Koethe R Conrad O Gross J Ringeler A Selige T 2002 Soil Regionalisation by Means of Terrain Analysis and Process Parameterisation In Micheli E Nachtergaele F Montanarella L ed Soil Classification 2001 European Soil Bureau Research Report No 7 EUR 20398 EN Luxembourg pp 213 222 See Also rsaga parallel processing rsaga geoprocessor rsaga env set file extension Examples Not run using SAGA grids
21. values from the input grid file that should be converted to NA in addition to the nodata value specified in the grid header out nodata value numeric value used for storing NAs in the output file s if missing use the same nodata value as specified in the header of the input grid file na strings passed on to scan search mode character either circle default for a circular search window or square for a squared one digits numeric specifying the number of digits to be used for output grid file dec character specifying the decimal mark to be used for input and output quiet If TRUE gives some output after every 10th line of the grid file and when the job is done nlines Number of lines to be processed useful for testing purposes mw to vector logical Should the content of the moving window be coerced from a matrix to a vector mw na rm logical Should NAs be removed from moving window prior to passing the data p to fun Only applicable when mw to vector TRUE Arguments to be passed to fun local function arguments to be passed to focal function Details focal function passes a square matrix of size 2xradius 1 to the function unif mw to vector FALSI default or a vector of length lt 2 radius 1 2 ifmw to vector TRUE This matrix or vector will contain the content of the moving window which may possibly contain NAs even if the in grid has no nodata values e g due to edge effects If s
22. 1 had a bug that made it impossible to pass a range of days of the year or a range of hours of the day time range to SAGA These options work in SAGA 2 0 1 This function uses module 2 from SAGA library ta_lighting Author s Alexander Brenning R interface Olaf Conrad SAGA module References Wilson J P Gallant J C eds 2000 Terrain analysis principles and applications New York John Wiley amp Sons See Also rsaga hillshade rsaga insolation Examples Not run potential solar radiation on Nov 7 in Southern Ontario rsaga solar radiation dem solrad soldur latitude 43 62 rsaga target days list day 7 month 11 time step 0 5 in fact a cold cloudy windy day End Not run rsaga target Define target grid for interpolation Description Define the resolution and extent of a target grid for interpolation by SAGA modules based on 1 fitting the extent to the input data 2 an existing SAGA grid file 3 user defined parameters or 4 the header data of an ASCII grid Intended to be used with RSAGA s interpolation functions WARNING THIS FUNCTION LIKELY DOESN T WORK WITH SAGA GIS 2 0 5 BECAUSE OF A CHANGE IN THE PARAMETERIZATION OF TARGET GRIDS Usage rsaga target target c user defined grid system target grid header user cellsize 100 user fit extent TRUE user x extent user y extent user bbox system nx system ny system xy system d ta
23. 3 41 rsaga hillshade 29 35 38 42 44 48 60 70 INDEX rsaga html help 37 38 43 write Rd grid read ascii grid rsaga import gdal 44 19 rsaga insolation 43 46 60 write sgrd read ascii grid 19 rsaga inverse distance 48 53 62 rsaga linear combination rsaga grid calculus 39 rsaga local morphometry 38 50 rsaga modified quadratic shephard 62 rsaga modified quadratic shephard rsaga inverse distance 48 rsaga nearest neighbour 62 rsaga nearest neighbour rsaga inverse distance 48 rsaga ordinary kriging 50 52 62 rsaga parallel processing 51 54 63 rsaga plan curvature rsaga local morphometry 50 rsaga profile curvature rsaga local morphometry 50 rsaga search modules 35 44 rsaga search modules rsaga get modules 36 rsaga sgrd to esri 29 30 56 rsaga sink removal 32 57 59 rsaga sink route 32 57 58 rsaga slope rsaga local morphometry 50 rsaga solar radiation 43 48 59 rsaga target 49 53 61 rsaga triangulation rsaga inverse distance 48 rsaga wetness index 55 62 scan 5 14 17 20 set file extension 64 system 18 34 35 wind shelter 7 65 write ascii grid 18 write ascii grid read ascii grid 19
24. A functions rsaga ordinary kriging rsaga inverse distance rsaga nearest neighbour and rsaga modified quadratic shephard Author s Alexander Brenning See Also read ascii grid header Examples Not run Krige attribute 0 from the points shapefile to a grid with the same extent and resolutionn as the pre existing geology grid rsaga ordinary kriging points dem field 0 maxdist 1000 target rsaga target target target grid target grid geology Specify a target grid manually see above rsaga ordinary kriging points dem field 0 radius 1000 target rsaga target grid system system nx 200 system ny 300 system xy c 604853 7465013 system d 50 End Not run rsaga wetness index SAGA Modules SAGA Wetness Index Description Calculate the SAGA Wetness Index SWI a modified topographic wetness index TWI Usage rsaga wetness index in dem out wetness index out carea out cslope out mod carea t param 64 rsaga wetness index Arguments in dem input digital elevation model DEM as SAGA grid file default file extension Sgrd out wetness index output optional wetness index grid Existing files of the same name will be overwritten out carea output optional catchment area out cslope output optional catchment slope out mod carea output optional modified catchment area t param positive numeric value optional
25. Arguments in sgrds character vector of SAGA grid files sgrd to be converted files are expected to be found in folder xsaga env workspace or if an optional env argument is provided in env workspace out grids character vector of ESRI ASCII float output file names defaults to in sgrds with the file extension being replaced by asc or 1t dependingon format Files will be placed in folder out pat h existing files will be overwritten out path folder for out grids format output file format either ascii default equivalent format 1 for ASCII grids or binary equivalent 0 for binary ESRI grids 1t georef character corner equivalent numeric code 0 or center default equivalent 1 Determines whether the georeference will be related to the center or corner of its extreme lower left grid cell prec number of digits when writing floating point values to ASCII grid files either a single number to be replicated if necessary or a numeric vector of length length in grids optional arguments to be passed to rsaga geoprocessor including the env RSAGA geoprocessing environment Value The type of object returned depends on the intern argument passed to the rsaga geoprocessor For intern FALSE it is a numerical error code 0 success or otherwise default a character vector with the module s console output Note This function uses module 0 from the SAGA library io grid Author s Alexander Brenning R int
26. E Gl write ascii grid data file header NULL write header TRUI digits dec georef corner write ascii grid header file header georef dec write sgrd data file header NULL prec 7 georef corner write Rd grid data file header NULL write header TRUE compress TRUE Arguments file file name of an ASCII grid extension defaults to asc if not specified or a connection open for reading or writing as required fname file name of a grid stored as an R Rd file extension defaults to Rd return header logical should the grid header be returned default or just the grid data matrix In the former case read ascii grid returns a list with two components named data and header print numeric specifying how detailed the output reporting the progress should be currently 0 to 2 0 being minimum output nodata values optional numeric vector specifying nodata values to be used in addition to the nodata value specified in the grid header nodata values are converted to NA at once logical if TRUE read the whole grid with one scan command if FALSE read it row by row using scan with option nlines 1 data grid data a data matrix or a list with components data the grid data matrix and header the grid header information header optional list argument specifying the grid header information as returned by the read ascii gridorread ascii grid header func
27. Package RSAGA August 26 2010 Type Package Title SAGA Geoprocessing and Terrain Analysis in R Version 0 91 1 Date 2010 08 25 Author Alexander Brenning Maintainer Alexander Brenning lt brenning uwaterloo ca gt Description RSAGA provides access to geocomputing and terrain analysis functions of SAGA from within R by running the command line version of SAGA In addition several R functions for handling and manipulating ASCII grids are provided including a flexible framework for applying local functions including predict methods of fitted models or focal functions to multiple grids SAGA is available under GPL via http sourceforge net projects saga gis License GPL 2 SystemRequirements SAGA gt 2 0 2 Suggests gstat shapefiles Repository CRAN Date Publication 2010 08 26 06 42 40 R topics documented RSAGA package LL 2 cemtervalue 3 create variablename 2 22 2 ll ee 4 focal function LL 5 pid predict MP 8 STIG AOR VA a 2o doo tn aea e det ae m d dei ene aub siae ae dosi 10 tatchi arg ext is susc pu a bo SE ey Ge eG RC ede sg pud we A 11 multi focal funetion LL 13 Pick Trom POMS paglia A ERI a 17 2 RSAGA package redd ascl gfid s s iu gii aa Ron XO Sox s Ra v 20 relative POSITION i eoa oec o AR E RR dL YU URN RUN a eR Te Oba CIRC 22 Fesid Median go gk ke eR ee Pa ees v E rj Re E SACR E we Pes 23 rsaga add grid values to points ooo 24 TSapa Close gaps 4 s sope ee
28. RUE default the console output of SAGA is returned as a character vector This character vector lists the input file names and modules arguments and gives a more or less de tailed report of the function s progress Redundant information can be cancelled out by setting reduce intern TRUE Note Existing output files will be overwritten by SAGA without prompting If a terrain analysis function is not directly interfaced by one of the RSAGA functions you might still find it in the growing set of SAGA libraries and modules The names of all libraries available in your SAGA installation can be obtained using xsaga get libraries or by checking the di rectory listing of the modules folder in the SAGA directory The names and numeric codes of all available modules globally or within a specific library are retreived by rsaga get modules Full text search in library and module names is performed by rsaga search modules For in formation on the usage of SAGA command line modules see rsaga get usage or the RSAGA interface function if available display command TRUE is mainly intended for debugging purposes to check if all arguments are passed correctly to SAGA CMD Author s Alexander Brenning R interface Olaf Conrad and the SAGA development team SAGA develop ment See Also rsaga env rsaga get libraries rsaga get modules rsaga search modules rsaga get usage rsaga esri wrapper for a wrapper for ESRI ASCII binary grids
29. a circular search window or square for a squared one numeric specifying the number of digits to be used for output grid file character specifying the decimal mark to be used for input and output If TRUE gives some output after every 10th line of the grid file and when the job is done Number of lines to be processed useful for testing purposes logical Should the content of the moving window be coerced from a matrix to a vector multi focal function 15 mw na rm logical Should NAs be removed from moving window prior to passing the data to fun Only applicable when mw to vector TRUE pass location logical Should the x y coordinates of grid points center of grid cells be passed to fun If TRUE two additional arguments named arguments x and y are passed to fun NOTE This currently only works for radius 0 otherwise a warning is produced and pass location is reset to FALSE na strings passed on to scan Arguments to be passed to fun local function arguments to be passed to focal function Details multi focal functionis probably most useful for applying the predict method of a fitted model to a grids representing the predictor variables An example is given below and in more detail in Brenning 2008 see also grid predict multi focal function extends focal function by allowing multiple input grids to be passed to the focal function fun operating on moving windows It passes square matric
30. a inverse distance func tion is trying to adapt to this situation If using a different SAGA GIS version try one of the two supported options or look at rsaga get modules grid_gridding and use rsaga geoprocessor directly sorry for the inconvenience Optional arguments to be passed to rsaga geoprocessor including the env RSAGA geoprocessing environment Details Inverse distance weighting IDW uses module 0 in the SAGA library grid gridding Nearest neighbour interpolation uses module 1 and triangulation is performed by module 4 Note The Inverse Distance Weighted module of SAGA GIS library grid_gridding has changed from SAGA GIS 2 0 4 to 2 0 5 The module now not only support inverse distance weighted interpola tion but also exponential and other weighting schemes command line argument WEIGHTING these are however not accessible through this function but only through the rsaga geoprocessor See rsaga get usage grid gridding Inverse Distance Weighted forde tails This R function furthermore only interfaces the local version of IDW which uses a local search radius argument radius the SAGA module now 2 0 5 also supports global IDW See the example section in the help file for write shapefile in package shapefiles to learn how to apply these interpolation functions to a shapefile exported from a data frame Modified Quadratic Shephard method based on module 660 in TOMS see references Au
31. a wetness index 62 Topic package 68 focal function 4 grid predict 7 grid to xyz 10 multi focal function 12 pick from points l6 read ascii grid 19 relative position 21 resid median 22 RSAGA package 2 rsaga add grid values to points 23 rsaga close gaps 24 rsaga contour 25 rsaga env 26 rsaga esri to sgrd 27 rsaga esri wrapper 28 rsaga fill sinks 30 rsaga filter gauss 32 rsaga filter simple 33 rsaga geoprocessor 34 rsaga get modules 36 rsaga get usage 38 rsaga grid calculus 39 rsaga grid to points 4l rsaga hillshade 42 rsaga import gdal 44 rsaga insolation 46 rsaga inverse distance 48 rsaga local morphometry 50 rsaga ordinary kriging 52 rsaga parallel processing 54 rsaga sgrd to esri 56 rsaga sink removal 57 rsaga sink route 58 rsaga solar radiation 59 rsaga target 6l rsaga wetness index 62 INDEX wind shelter 65 Topic utilities centervalue 3 create variable name 3 match arg ext 11 rsaga html help 43 set file extension 64 abbreviate 6 browseURL 44 centervalue 3 2 22 create variable name 3 7 17 default file extension set file extension 64 focal function 3 4 9 14 15 21 22 41 65 66 gapply focal function 4 get file extension set file extension 64 grid predict 7 9 12 15 grid to xyz 10 8 local function 4 local function focal function 4 match arg 11 12 match arg ext ll median 22 multi focal fun
32. as and 80 percent deserts pressure atmospheric pressure in mbar rsaga solar radiation 61 water content water content of a vertical slice of the atmosphere in cm between 1 5 and 1 7cm average 1 68cm default dust dust factor in ppm defaults to 100ppm time range numeric vector of length 2 time span hours of the day for numerical integra tion time step time step in hours for numerical integration days either a list with components day and month specifying a single day of the year for radiation modeling OR a numeric vector of length 2 specifying the start and end date see Note below day step if days indicates a range of days this specifies the time step number of days for calculating the incoming solar radiation optional arguments to be passed to rsaga geoprocessor including the env RSAGA geoprocessing environment Note SAGA uses zero based days and months but this R function uses the standard one based days and months e g day 1 is the first day of the month month 1 is January and translates to the SAGA system In SAGA 2 0 2 solar radiation sums calculated for a range of days say days c a b actually calculate radiation only for days a 1 in steps of day step I used day step 1 in this example The setting a b however gives the same result as b a 1 and indeed b a 2 gives twice the radiation sums and potential sunshine duration that a b and b a 1 both give The solar radiation module of SAGA 2 0
33. ble names to be used for naming the output grids For the input files asc is used as the default file extension if it is not specified by the user See focal function for details Value multi focal function returns the character vector of output file names Note multi focal function can do all the things focal function can do 16 multi focal function Author s Alexander Brenning References Brenning A 2008 Statistical geocomputing combining R and SAGA The example of land slide susceptibility analysis with generalized additive models In J Boehner T Blaschke L Montanarella eds SAGA Seconds Out Hamburger Beitraege zur Physischen Geographie und Landschaftsoekologie 19 23 32 http www environment uwaterloo ca u brenning Brenning 2008 RSAGA pdf See Also focal function grid predict Examples Not run Assume that d is a data frame with point observations of a numerical response variable y and predictor variables a b and c Fit a generalized additive model to y a b c We want to model b and c as nonlinear terms require gam fit gam y a s b s c data d multi focal function in grids c a p c out varnames pred fun grid predict fit fit Note that the grid predict uses by default the predict method of fit Model predictions are written to a file named pred asc End Not run Not run A fake example of a logistic additi
34. calculus elevation sgrd maat sgrd 20 0 6 a End Not run rsaga grid to points Convert SAGA grid file to point shapefile Description Convert SAGA grid file to point shapefile either completely or only a random sample of grid cells Usage rsaga grid to points in grids out shapefile in clip polygons exclude nodata TRUE rsaga grid to points randomly in grid out shapefile freq Arguments in grids Input names of possibly several SAGA grid files to be converted into a point shapefile in grid Input SAGA grid file from which to sample out shapefile Output point shapefile default extension shp Existing files will be over written in clip polygons optional polygon shapefile to be used for clipping masking an area exclude nodata logical default TRUE skip nodata grid cells rsaga hillshade 43 freq integer gt 1 sampling frequency on average 1 out of freq grid cells are se lected Optional arguments to be passed to rsaga geoprocessor including the env RSAGA geoprocessing environment Note These functions use modules 3 and 4 in SAGA library shapes grid Author s Alexander Brenning R interface Olaf Conrad SAGA modules See Also rsaga add grid values to points Examples Not run rsaga grid to points randomly dem dempoints freq 20 End Not run rsaga hillshade Analytical hillshading Description Analyt
35. contents of a square or circular moving window to these functions The resid median function rests the value of the central grid cell from the median of the whole moving window Thus in terms of topography a positive residual median indicates that this grid cell stands out compared to its surroundings resid quantile gives more flexibility in designing such residual attributes Value If x is provided a numeric vector of length 1 resid median 3 resid minmedmax and resid quartiles or length probs resid quantile If x is missing a character vector of same length giving suggested variable or file names such as rmed See focal function for details Author s Alexander Brenning See Also focal function quantile median centervalue 24 rsaga add grid values to points rsaga add grid values to points Add Grid Values to Point Shapefile Description Pick values from SAGA grids and attach them as a new variables to a point shapefile THIS SAGA MODULE CURRENTLY SEEMS TO CRASH SAGA but not R Usage rsaga add grid values to points in shapefile in grids out shapefile method c nearest neighbour bilinear idw bicubic spline b spline Arguments in grids Input character vector with names of one or more SAGA grid files to be converted into a point shapefile in shapefile out shapefile In Output point shapefiles default extension shp method interpolation method to be us
36. ction 7 8 12 41 pick from ascii grid 10 23 pick from ascii grid pick from points 16 pick from points 16 23 pick from saga grid 23 pick from saga grid pick from points 16 pick from shapefile pick from points 16 pmatch 11 12 predict 8 quantile 22 66 rank 21 read ascii grid 0 18 19 69 read ascii grid header 62 read Rd grid read ascii grid 19 read sgrd read ascii grid 19 relative position 7 21 relative rank 7 relative rank relative position 21 resid median 3 7 22 resid minmedmax 6 7 resid minmedmax resid median 22 resid quantile 6 7 resid quantile resid median 22 resid quartiles 7 resid quartiles resid median 22 RSAGA RSAGA package 2 RSAGA package 2 rsaga add grid values to points 23 42 rsaga aspect rsaga local morphometry 50 rsaga close gaps 24 29 rsaga close one cell gaps rsaga close gaps 24 rsaga contour 25 rsaga curvature rsaga local morphometry 50 rsaga env 2 18 24 26 28 30 34 38 41 44 51 55 57 63 rsaga esri to sgrd 27 29 30 rsaga esri wrapper 28 28 35 57 rsaga fill sinks 30 57 58 rsaga filter gauss 32 33 rsaga filter simple 32 33 rsaga geoprocessor 8 23 25 28 33 34 37 44 47 51 53 58 60 63 rsaga get lib modules rsaga get modules 36 rsaga get libraries 35 rsaga get libraries rsaga get modules 36 rsaga get modules 35 36 44 rsaga get usage 35 37 38 44 rsaga grid calculus 39 rsaga grid to points 2
37. ds provided as ESRI grids in esri TRUE or as SAGA grids logical should output grids be converted to ESRI grids RSAGA environment as returned by rsaga env esri workspace format georef prec directory for the input and output ESRI ASCII binary grids output file format either ascii default equivalent format 1 for ASCII grids or binary equivalent 0 for binary ESRI grids 1t character corner equivalent numeric code 0 or center default equivalent 1 Determines whether the georeference will be related to the center or corner of its extreme lower left grid cell number of digits when writing floating point values to ASCII grid files only relevant if out esri TRUE esri extension extension for input output ESRI grids defaults to asc for format ascii andto flt for format binary condensed res clean up intern Details logical return only results of the RSAGA geoprocessing function fun condensed res TRUE or include the results of the import and export operations i e the calls to rsaga esri to sgrdandrsaga sgrd to esri see Value logical delete intermediate SAGA grid files intern argument to be passed to rsaga geoprocessor see Value additional arguments for fun NOTE ESRI ASCII float raster file names should NOT include the file extension asc flt the file extension is defined by the esri extension and format arguments ESRI ASCII float raster file names s
38. e corner of the lower left grid cell cellsize Single numeric value specifying the size of a grid cell or pixel in both x and y direction nodata value Single numeric value being interpreted as NA typically 9999 xllcenter X coordinate of the center of the lower left grid cell yllcenter y coordinate of the center of the lower left grid cell Note The order of the components especially of 11corner and llcenter may change depending on the order in which they appear in the grid header and on the georeferencing method center or corner used for the grid The 11corner and 11center attributes differ only by cellsize 2 Note The read Rd grid and write Rd grid functions use the load and save commands to store a grid The variable name used is data which is either a numeric matrix or a list with components data the grid data matrix and header the grid header information Author s Alexander Brenning 22 relative position See Also write ascii grid write ascii grid header read Rd grid relative position Relative Topographic Position Description relative position and relative rank are used with focal function to determine the relative value of a grid cell compared to its surroundings either on a metric scale or based on ranks Usage relative position x relative rank x ties method average Arguments x a square matrix with the grid data from the moving window possibly containing NA values
39. earch mode circle values more than radius units pixels or grid units depending on is pixel radius away from the center pixel matrix entry will be set to NA In addition valid range nodata values and the nodata values specified in the in grid are checked to assign further NAs to pixels in the mov ing window Finally if in factor grid specifies zones all pixels in the moving window that belong to a different zone than the center pixel are set to NA or in other words zone boundaries are used as breaklines The function un should return a single numeric value or a numeric vector As an example the function resid minmedmax returns the minimum median and maximum of the difference be tween the values in the moving window and the value in the center grid cell In addition to the first argument receiving the moving window data fun may have additional arguments the argument of focal function is passed on to fun resid quantile is a function that uses this feature G focal function 7 Optionally fun should support the following feature If no argument is passed to it then it should return a character vector giving variable names to be used for naming the output grids The call resid minmedmax for example returns c rmin rmed rmax this vector must have the same length as the numeric vector returned when moving window data is passed to the function This feature is only used if no varnames argument is pr
40. ed choices nearest neighbour interpolation de fault bilinear interpolation inverse distance weighting bicubic spline interpo lation B splines Optional arguments to be passed to xsaga geoprocessor including the env RSAGA geoprocessing environment Details Retrieves information from the selected grids at the positions of the points of the selected points layer and adds it to the resulting layer Note This function uses module 0 in SAGA library shapes grid Author s Alexander Brenning R interface Olaf Conrad SAGA modules See Also pick from points pick trom ascili grid pick from sagad grid rsaqga grid to points rsaga close gaps 25 rsaga close gaps SAGA Modules Close Gaps and Close One Cell Gaps Description Close Interpolate Gaps Usage rsaga close gaps in dem out dem threshold 0 1 rsaga close one cell gaps in dem out dem Arguments in dem input digital elevation model DEM as SAGA grid file default file extension Sgrd out dem output DEM grid file without no data values gaps Existing files will be over written threshold tension threshold for adjusting the interpolator default 0 1 optional arguments to be passed to rsaga geoprocessor including the env RSAGA geoprocessing environment Details rsaga close one cell gaps only fill gaps whose neighbor grid cells have non missing data In rsaga close gaps larger tension thresholds can be used to reduce overshoots and
41. erface Olaf Conrad SAGA module 58 rsaga sink removal See Also rsaga esri wrapper for an efficient way of applying RSAGA to ESRI ASCII binary grids rsaga env rsaga sink removal Sink Removal Description Remove sinks from a digital elevation model by deepening drainage routes or filling sinks Usage rsaga sink removal in dem in sinkroute out dem method fill Arguments in dem input digital elevation model DEM as SAGA grid file default file extension Sgrd in sinkroute optional input sink route grid file out dem output modified DEM method character string or numeric value specifying the algorithm partial string match ing will be applied deepen drainage route or 0 reduce the el evation of pixels in order to achieve drainage out of the former sinks fill sinks or 1 fill sinks until none are left optional arguments to be passed to rsaga geoprocessor including the env RSAGA geoprocessing environment Value The type of object returned depends on the intern argument passed to the rsaga geoprocessor For intern FALSE itis a numerical error code 0 success or otherwise default a character vector with the module s console output Note This function uses module 1 from SAGA library ta preprocessor Author s Alexander Brenning R interface Olaf Conrad SAGA module See Also rsaga sink route rsaga fill sinks rsaga sink route 59 Examples Not run rsaga sink rou
42. es of size 2 radius 1 to the function fun if mw to vector FALSE default or a vector of length lt 2xradius 1 2 if mw to vector TRUE one such matrix or vector per input grid will be passed to un as an argument whose name is specified by in varnames These matrices or vectors will contain the content of the moving window which may possibly con tain NAs even if the in gridhas no nodata values e g due to edge effects If search mode circle values more than radius units pixels or grid units depending on is pixel radius away from the center pixel matrix entry will be set to NA In addition valid range nodata values and the nodata values specified in the in grid are checked to assign further NAs to pixels in the moving window Finally if in factor grid specifies zones all pixels in the moving window that belong to a different zone than the center pixel are set to NA or in other words zone boundaries are used as breaklines The function fun should return a single numeric value or a numeric vector such as a regression result or a vector of class probabilities returned by a soft classifier In addition to the named argu ments receiving the moving window data fun may have additional arguments the argument of focal function is passed on to fun grid predict uses this feature Optionally fun should support the following feature If no argument is passed to it then it should return a character vector giving varia
43. es package The nearest neighbour interpolation currently randomly breaks ties if pick from points is used and in a deterministic fashion rounding towards greater grid indices i e toward south and east in the grid functions Author s Alexander Brenning References put references to the literature web site here See Also grid OZ Examples read ascii grid write ascii grid use the meuse data for some tests require gstat data meuse data meuse grid meuse nn pick from points data meuse grid src meuse pick c cadmium copper elev method nearest neighbour meuse kr pick from points data meuse grid src meuse pick c cadmium copper elev method krige radius 100 it does make a difference plot meuse krScadmium meuse nn cadmium plot meuse krScopper meuse nnScopper plot meuse kr elev meuse nn elev 20 read ascii grid read ascii grid Read write ASCII SAGA and Rd Grid Files Description These functions provide simple interfaces for reading and writing grids from to ASCII grids and Rd files Grids are stored in matrices their headers in lists Usage read ascii grid file return header TRUE print O0 nodata values c at once TRUE na strings NA read ascii grid header file read sgrd fname return header TRUE print 0 nodata values c at once TRUE prec 7 read Rd grid fname return header TRU
44. f mw to vector FALSE mw na rm FALSE pass location FALSE Arguments in grids character vector file names of input ASCII grids relative to in path in grid prefix will be used as a prefix to the file name if specified default file extension asc in factor grid optional file name giving a gridded categorical variables defining zones zone boundaries are used as breaklines for the moving window see Details in grid prefix character string optional defining a file name prefix to be used for the input file names a dash will separate the prefix and the in varnames 14 multi focal function out grid prefix path in path out path fun in varnames out varnames radius character string optional defining a file name prefix to be used for the output file names a dash will separate the prefix and the out varnames path in which to look for in grids and write output grid files see also in path and out path which overwrite path if they are specified path in which to look for in grids defaults to path path in which to write output grid files defaults to path a function or name of a function to be applied on the moving window see Details un is expected to accept named arguments with the names given by in varnames grid predict is a wrapper function that can be used for applying a model s predict method to a stack of grids see Details character vector names of the var
45. from grid digital elevation models Water Resources Research 27 709 717 Braunschweiger Reliefmodell Bauer J Rohdenburg H Bork H R 1985 Ein Digitales Reliefmodell als Vorraussetzung fuer ein deterministisches Modell der Wasser und Stoff Fluesse Landschaftsgenese und Landschaft soekologie H 10 Parameteraufbereitung fuer deterministische Gebiets Wassermodelle Grundla genarbeiten zu Analyse von Agrar Oekosystemen eds Bork H R Rohdenburg H p 1 15 Deterministic Infinity Tarboton D G 1997 A new method for the determination of flow directions and upslope areas in grid digital elevation models Water Ressources Research 33 2 309 319 Multiple Flow Direction Freeman G T 1991 Calculating catchment area with divergent flow based on a regular grid Computers and Geosciences 17 413 22 Quinn P F Beven K J Chevallier P Planchon O 1991 The prediction of hillslope flow paths for distributed hydrological modelling using digital terrain models Hydrological Processes 5 59 79 See Also rsaga wetness index rsaga geoprocessor rsaga env rsaga sgrd to esri 57 rsaga sgrd to esri Convert SAGA grids to ESRI ASCII binary grids Description rsaga sgrd to esri converts grid files from SAGA s version 2 grid format sgrd to ESRI s ASCII asc and binary flt format Usage rsaga sgrd to esri in sgrds out grids out path format ascii georef corner prec 5
46. geler SAGA module Frank Warmer dam GDAL References GDAL website http www gdal org See Also read ascii grid rsaga esri to sgrd read sgrd read Rd grid rsaga insolation Incoming Solar Radiation Insolation Description This function calculates the amount of incoming solar radiation insolation depending on slope aspect and atmospheric properties Usage rsaga insolation in dem in vapour in latitude in longitude out direct out diffuse out total horizontal FALSE solconst 8 164 atmosphere 12000 water vapour pressure 10 type c moment day range of days same moment range of days time step 1 day step 5 days moment latitude bending FALSE radius 6366737 96 lat offset user lat ref user 0 lon offset center lon ref user 0 48 Arguments in dem in vapour in latitude in longitude out direct out diffuse out total horizontal solconst atmosphere water vapour type time step day step days moment latitude bending radius lat of lat re lon of lon re fset f user fset f user rsaga insolation Name of input digital elevation model DEM grid in SAGA grid format default extension sgrd Optional input SAGA grid file giving the water vapour pressure in mbar Optional input SAGA grid file giving for each pixel the latitude in degree Optional input SAGA grid file giving fo
47. grid optional output flow path length grid integer gt 1 step parameter character or numeric choice of processing algorithm Deterministic 8 d8 or 0 Rho 8 rho8 or 1 Braunschweiger Reliefmodell braunschweig or 2 Deterministic Infinity dinf or 3 Multiple Flow Direction mfd or 4 default linear threshold convergence numeric number of grid cells threshold above which linear flow i e the De terministic 8 algorithm will be used linear flow is disabled for linear threshold Inf default numeric gt 0 a parameter for tuning convergent divergent flow default value of 1 1 gives realistic results and should not be changed further arguments to rsaga geoprocessor 56 rsaga parallel processing Details Refer to the references for details on the available algorithms Value The type of object returned depends on the intern argument passed to the rsaga geoprocessor For intern FALSE itis a numerical error code 0 success or otherwise default a character vector with the module s console output Note This function uses module 0 from SAGA library ta hydrology Author s Alexander Brenning R interface Olaf Conrad SAGA module References Deterministic 8 O Callaghan J F Mark D M 1984 The extraction of drainage networks from digital elevation data Computer Vision Graphics and Image Processing 28 323 344 Rho 8 Fairfield J Leymarie P 1991 Drainage networks
48. he northern hemisphere a northwesterly light source is required to properly depict relief in hillshading images Physically correct southerly light sources results a hillshade that would be considered by most people as inverted hills look like depressions mountain chains like troughs This function uses module 0 from SAGA library ta lighting Author s Alexander Brenning R interface Olaf Conrad SAGA module See Also rsaga solar radiation rsaga insolation Examples Not run rsaga hillshade dem sgrd hillshade rsaga html help HTML help on a SAGA module or library Description This function tries to obtain SAGA s HTML help for the specified library or module NOTE HTML help files are not provided with all SAGA distributions Usage rsaga html help lib module env rsaga env rsaga import gdal Arguments lib module env Details Doesn t seem to work with SAGA GIS 2 0 2 needs to be updated sorry Please use rsaga get usage 45 name of the SAGA library or one of the rsaga module functions such as rsaga hillshade name or numeric identifier of SAGA module in library lib module NULL links to the main help page of the SAGA library 1ib list setting up a SAGA geoprocessing environment as created by rsaga env additional arguments to be passed to browseURL or rsaga search modules orrsaga get modules instead Deprecated details on this function This help is not always available t
49. here are some mismatches between libraries and their HTML files and the HTML files are designed for use with SAGA GUI not with the command line version Some HTML help pages are also linked to the wrong module in this case the SAGA library s help page may provide a link to the module s help page In many cases rsaga get usage will provide more reliable information Author s Alexander Brenning See Also rsaga get usage rsaga geoprocessor rsaga env browseURL Examples Not run rsaga html help rsaga parallel processing rsaga import gdal Import Grid Files to SAGA grid format using GDAL Description These functions provide simple interfaces for reading and writing grids from to ASCII grids and Rd files Grids are stored in matrices their headers in lists Usage rsaga import gdal in grid out grid saga version 2 0 4 46 rsaga import gdal Arguments in grid file name of a grid in a format supported by GDAL out grid output SAGA grid file name defaults to in grid with the file extension being removed file extension should not be specified it defaults to sgrd saga version character string indicating the SAGA GIS version number currently only 2 0 4 and 2 0 5 are supported The reason for providing SAGA GIS version support is that some of the SAGA command line argument names have changed additional arguments to be passed to rsaga geoprocessor Details The GDAL Raster Import module of SAGA im
50. hould NOT include the file extension asc flt the file exten sion is defined by the esri extension and format arguments Value The object returned depends on the condensed res arguments and the intern argument passed to the rsaga geoprocessor If condensed res TRUE and intern FALSE a single numerical error code 0 success is returned If condensed res TRUE and intern TRUE default a character vector with the module s console output is returned invisibly If condensed res FALSE the result is a list with components in res geoproc res and out res Each of these components is either an error code for intern FALSE or for intern TRUE a character vector with the console output of the input rsaga esri to sgrd the geoprocess ing fun and the output conversion rsaga sgrd to esri step respectively For in esri FALS 1 or out esri FALSE the corresponding component is NULL rsaga fill sinks 31 Note Note that the intermediate grids as well as the output grids may overwrite existing files with the same file names without prompting the user See example below Author s Alexander Brenning See Also rsaga esri to sgrd rsaga sgrd to esri rsaga geoprocessor rsaga env Examples Not run rsaga esri wrapper rsaga hillshade in dem dem out grid hshd condensed res FALSE intern F if successful returns list in res 0 geoproc res 0 out res 0 and writes hshd asc intermediate f
51. iables corresponding to the in grids if missing same as in grids if specified must have the same length and order as in grids character vector specifying the name s of the variable s returned by fun if missing multi focal function will try to determine the varnames from fun itself or or from a call to un if this is a function see Details numeric value specifying the circular or square radius of the moving window see is pixel radius and search mode note that all data within dis tance lt radius will be included in the moving window not radius is pixel radius valid ranges logical if TRUE default the radius will be interpreted as a possibly non integer number of pixels if FALSE it is interpreted as a radius measured in the grid map units optional list of length length in grids with numeric vector of length 2 specifying minimum and maximum valid values read from input file all values lt valid ranges i 1 or gt valid ranges i 1 will be con verted to NA nodata values numeric vector any values from the input grid file that should be converted to NA in addition to the nodata value specified in the grid header out nodata value search mode digits dec quiet nlines mw to vector numeric value used for storing NAs in the output file s if missing use the same nodata value as specified in the header of the input grid file character either circle default for
52. ibs or character string Lib with the name s of library ies in which to look for modules if 1ibs is missing all libraries will be processed modules optional list result of rsaga get modules if missing a list of available modules will be retrieved using that function env list setting up a SAGA geoprocessing environment as created by rsaga env path path of SAGA library files modules subfolder in the SAGA installation folder defaults to the path determined by rsaga env 38 rsaga get modules dll file extension of dynamic link libraries interactive logical default FALSE should modules be returned that can only be executed in interactive mode i e using SAGA GUI Sv currently only interactive to be passedonto rsaga get lib modules Value rsaga get libraries returns a character vector with the names of all SAGA libraries avail able in the folder env modules rsaga get lib modules returns a data frame with name the names of all modules in library lib code their numeric identifiers interactive anda logical variable indicating whether a module can only be executed in in teractive SAGA GUI mode rsaga get modules returns a list with for each SAGA library in libs adata frame with module information as given by rsaga get lib modules If libs is missing all modules in all libraries will be retrieved Note For information on the usage of SAGA command line modules see rsaga get usage or rsaga html help orthe RSAGA interface func
53. ical hillshading calculation Usage rsaga hillshade in dem out grid method standard azimuth 315 declination 45 exaggeration 4 Arguments in dem Input digital elevation model DEM as SAGA grid file default extension sgrd out grid Output hillshading grid SAGA grid file Existing files will be overwritten method Available choices character or numeric standard or 0 default max90deg standard 1 combined shading 2 ray tracing 3 See Details azimuth Direction of the light source measured in degree clockwise from the north di rection default 315 i e northwest declination Declination of the light source measured in degree above the horizon default 45 44 rsaga html help exaggeration Vertical exaggeration of elevation default 4 The terrain exaggeration factor allows to increase the shading contrasts in flat areas Optional arguments to be passed to rsaga geoprocessor including the env RSAGA geoprocessing environment Details The Analytical Hillshading algorithm is based on the angle between the surface and the incoming light beams measured in radians Value The type of object returned depends on the intern argument passed to the rsaga geoprocessor For intern FALSE itis a numerical error code 0 success or otherwise default a character vector with the module s console output Note While the default azimuth of 315 degree northwest is not physically meaningful on t
54. iles dem sgrd dem hgrd dem sdat hshd sgrd hshd hgrd and hshd sdat are deleted hshd asc is overwritten if it already existed End Not run rsaga fill sinks Fill Sinks Description Several methods for filling closed depressions in digital elevation models that would affect hydro logical modeling Usage rsaga fill sinks in dem out dem method planchon darboux 2001 out flowdir out wshed minslope Arguments in dem Input digital elevation model DEM as SAGA grid file default extension sgra out dem Output filled depression free DEM SAGA grid file Existing files will be overwritten method The depression filling algorithm to be used character One of planchon darboux 2001 default wang 1iu 2006 or xxl wang liu 2006 out flowdir only for wang liu 2001 Optional output grid file for computed flow directions see Notes out wshed only for wang 1iu 2001 Optional output grid file for watershed basins 32 rsaga fill sinks minslope Minimum slope angle in degree preserved between adjacent grid cells default value of 0 01 only for method planchon darboux 2001 otherwise no default Optional arguments to be passed to rsaga geoprocessor including the env RSAGA geoprocessing environment Details This function bundles three SAGA modules for filling sinks using three different algorithms method argument planchon darboux 2001 The algorithm of Pla
55. in the PATH environment variable defaults to FALSE on non Windows OS check os default if TRUE look for SAGA in the folder specified by os de ault path os default path C Progra 1 SAGA GIS under Windows or usr local bin under unix Details rsaga env tries to compile infromation on the SAGA environment this is not easy because there is no standard installation folder and procedure If path is missing rsaga env first looks for an environment variable SAGA if this is undefined it checks the current working di rectory then the paths given in the PATH environment variable and finally the function s guess is C Progra 1 SAGA GIS or usr local bin on non Windows systems 28 rsaga esri to sgrd The default modules folder under Windows is the modules subfolder of the SAGA binaries folder The SAGA MLB environment variable is not being checked Under Unix the default modules folder is usr local lib saga Value A list with components workspace cmd path and modules with values as passed to rsaga env or default values as described in the Details section Note Note that the default workspace is not getwd ie the default SAGA workspace folder is not fixed it changes each time you change the R working directory using set wd The default SAGA folder used to be C Progra 1 saga_vc now itis C Progra 1 SAGA GIS because the most recent SAGA version installs by default in this folder Author
56. ing environment i e currently a list with information on the SAGA and SAGA modules paths and the name of the working directory in which to look for input and output files Defaults see rsaga env display command Display the DOS command line for executing the SAGA module including all the arguments to be passed Default FALSE reduce intern If intern TRUE reduce the text output of SAGA returned to R by eliminating redundant lines showing the progress of module execution etc default TRUE Additional arguments to be passed to system 36 rsaga geoprocessor Details This workhorse function establishes the interface between the SAGA command line program and R by submitting a system call This is a low level function that may be used for directly accessing SAGA specific functions such as rsaga hillshade are intended to be more user friendly in terfaces to the most frequently used SAGA modules These higher level interfaces support default values for the arguments and perform some error checking they should therefore be preferred if available Value The type of object returned depends on the intern argument passed to syst em If intern FALSE a numerical error success code is returned where a value of 0 corresponds to success and a non zero value indicates an error Note however that the function always returns a success value of 0 if wait FALSE ie if it does not wait for SAGA to finish If intern T
57. iogram range numeric for method krige only the nugget effect for method krige only the variogram model to be used for interpola tion defaults to a spherical variogram with parameters specified by the range sill and nugget arguments see vgm in package gstat for details logical vector specifying for each variable in pick if interpolation should take place on the logarithmic scale default FALSE X name Y name cbind file path varname prefix names of the variables containing the x and y coordinates logical shoud the new variables be added to the input data frame cbind TRUE the default or should they be returned as a separate vector or data frame cbind FALSE file name relative to pat h default file extension asc of an ASCII grid from which to pick a variable or an open connection to such a file optional path to ile character string a variable name for the variable interpolated from grid file fileinpick from grid if missing variable name will be determined from filename by a call to create variable name an optional prefix to be added to the varname nodata values at once quiet nlines filename prec na strings env show output numeric vector specifying grid values that should be converted to NA in addition to the values specified here the nodata value given in the input grid s header will be used logical should the grid be read as a whole or line by line a
58. lanetary radius latitude relates to grids bottom equivalent code 0 center 1 top 2 or user defined reference default user in the latter case lat ref user defines the reference if in latitude is missing and lat offset user then this numeric value defines the latitudinal reference details local time refers to grid s left edge code 0 center 1 right edge 2 or a user defined reference if in longitude is missing and lon offset user then this numeric value defines the reference of the local time details optional arguments to be passed to rsaga geoprocessor including the env RSAGA geoprocessing environment rsaga inverse distance 49 Details Calculation of incoming solar radiation insolation Based on the SADO System for the Analysis of Discrete Surfaces routines developed by Boehner amp Trachinow Value The type of object returned depends on the intern argument passed to the rsaga geoprocessor For intern FALSE itis a numerical error code 0 success or otherwise default a character vector with the module s console output Note This function uses module 3 from SAGA library ta 1ighting Author s Alexander Brenning R interface Olaf Conrad SAGA module See Also rsaga solar radiation rsaga hillshade rsaga inverse distance Spatial Interpolation Methods Description Spatial interpolation of point data using inverse distance to a power inver
59. n asc rsaga esri wrapper rsaga slope in dem lican out slope slope method maxslope Ht End Not run rsaga ordinary kriging Local Ordinary Kriging Description Perform ordinary kriging using a local search neighborhood local ordinary kriging Also supports block kriging Usage rsaga ordinary kriging in shapefile out grid out variance grid field model c spherical exponential gaussian nugget 0 sill 10 range 100 log transform FALSE maxdist 1000 blocksize nmin 4 nmax 20 target rsaga target Arguments in shapefile Input point shapefile default extension shp out grid Output filename for interpolated grid SAGA grid file Existing files will be overwritten out variance grid Output optional SAGA grid for kriging variances field numeric number not name of attribute in the shapefile s attribute table to be interpolated the first attribute is represented by a zero model character variogram model to be used defaults to spherical nugget numeric 2 0 Nugget effect sill numeric gt 0 Sill of the variogram range numeric gt 0 Variogram range log transform logical apply a log transformation to the observations default FALSE maxdist numeric maximum distance of nearest points to be used for kriging search radius nmin numeric Minimum number of points within the local search neighborhood requi
60. nchon and Darboux 2001 consists of in creasing the elevation of pixels in closed depressions until the sink disappears and a mininum slope angle of minslope default 0 01 degree is established wang liu 2006 This module uses an algorithm proposed by Wang and Liu 2006 to iden tify and fill surface depressions in DEMs The method was enhanced to allow the creation of hydrologically sound elevation models i e not only to fill the depressions but also to preserve a downward slope along the flow path If desired this is accomplished by preserving a minimum slope gradient and thus elevation difference between cells This is the fully featured version of the module creating a depression free DEM a flow path grid and a grid with watershed basins If you encounter problems processing large data sets e g LIDAR data with this module try the basic version xxl wang lui 2006 xxl wang liu 2006 This modified algorithm after Wang and Liu 2006 is designed to work on large data sets Value The type of object returned depends on the intern argument passed to the rsaga geoprocessor For intern FALSE itis a numerical error code 0 success or otherwise default a character vector with the module s console output The function writes SAGA grid files containing of the depression free preprocessed DEM and optionally the flow directions and watershed basins Note The flow directions are coded as 0 north 1 northeast 2 east
61. nts dem field 0 maxdist 1000 target rsaga target target target grid target grid geology Specify a target grid manually see rsaga target rsaga ordinary kriging points dem field 0 radius 1000 target rsaga target grid system system nx 200 system ny 300 system xy c 604853 7465013 system d 50 End Not run rsaga parallel processing 55 rsaga parallel processing Parallel Processing Description Calculate the size of the local catchment area contributing area the catchment height catchment slope and aspect and flow path length using parallel processing algorithms including the recom mended multiple flow direction algorithm This set of algorithms processes a digital elevation model DEM downwards from the highest to the lowest cell Usage rsaga parallel processing in dem in sinkroute in weight out carea out cheight out cslope out caspect out flowpath step method mfd linear threshold Inf convergence 1 1 Arguments in dem input digital elevation model DEM as SAGA grid file default file extension in sinkroute in weight out carea out cheight out cslope out caspect out flowpath step method Sgrd optional input SAGA grid with sink routes optional intput SAGA grid with weights output catchment area grid optional output catchment height grid optional output catchment slope grid optional output catchment aspect
62. or the moving window see Details out grid prefix character string optional defining a file name prefix to be used for the output file names a dash will separate the prefix and the varnames path path in which to look for in grid and write output grid files see also in path and out path which overwrite path if they are specified in path path in which to look for in grid defaults to path out path path in which to write output grid files defaults to path fun a function or name of a function to be applied on the moving window see Details varnames character vector specifying the names of the variable s returned by fun if missing focal function will try to determine the varnames from fun it self or or from a call to fun if this is a function see Details radius numeric value specifying the circular or square radius of the moving window see is pixel radius and search mode note that all data within dis tance lt radius will be included in the moving window not lt radius focal function is pixel radius logical if TRUE default the radius will be interpreted as a possibly non integer number of pixels if FALSE it is interpreted as a radius measured in the grid map units valid range numeric vector of length 2 specifying minimum and maximum valid values read from input file all values lt valid range 1 or gt valid range 1 will be converted to NA nodata values numeric vector any
63. ources Research 33 2 309 319 Least Squares or Bes t Fit Plane Beasley D B Huggins L F 1982 ANSWERS User s manual U S EPA 905 9 82 001 Chicago IL 54 pp Costa Cabral M Burges S J 1994 Digital Elevation Model Networks DEMON a model of flow over hillslopes for computation of contributing and dispersal areas Water Resources Research 30 6 1681 1692 Fit 2nd Degree Poly nomial Bauer J Rohdenburg H Bork H R 1985 Ein Digitales Re liefmodell als Vorraussetzung fuer ein deterministisches Modell der Wasser und Stoff Fluesse Landschaftsgenese und Landschaftsoekologie H 10 Parameteraufbereitung fuer deterministische Gebiets Wassermode lle Grundlagenarbeiten zur Analyse von Agrar Oekosystemen eds Bork H R Rohdenburg H p 1 15 Heerdegen R G Beran M A 1982 Quantifying source areas through land surface curvature Journal of Hydrology 57 Zevenbergen L W Thorne C R 1987 Quantitative analysis of land surface topography Earth Surface Processes and Landforms 12 47 56 Fit 3 Degree Polynom Haralick R M 1983 Ridge and valley detection on digital images Com puter Vision Graphics and Image Processing 22 1 28 38 See Also rsaga parallel Examples Not run processing rsaga geoprocessor rsaga env a simple slope algorithm rsaga slope lican sgrd slope maxslope rsaga ordinary kriging 53 same for ASCII grids default extensio
64. ovided Note that the result is currently being abbreviated to a length of 6 characters Input and output file names are built according to the following schemes Input lt in path gt lt in grid gt Zones lt in path gt lt in factor grid gt if speci fied Output lt out path gt lt out grid prefix gt lt varnames gt asc For the input files asc is used as the default file extension 1f it is not specified by the user Value focal function and local function return the character vector of output file names Note These functions are not very efficient ways of calculating e g focal terrain attributes compared to for example the SAGA modules but the idea is that you can easily specify your own functions without starting to mess around with C code For example try implementing a median filter as a SAGA module or just use the code shown in the example Author s Alexander Brenning References Brenning A 2008 Statistical geocomputing combining R and SAGA The example of land slide susceptibility analysis with generalized additive models In J Boehner T Blaschke L Montanarella eds SAGA Seconds Out Hamburger Beitraege zur Physischen Geographie und Landschaftsoekologie 19 23 32 http www environment uwaterloo ca u brenning Brenning 2008 RSAGA pdf See Also multi focal function resid median resid minmedmax relative position resid quantile resid quartiles relative rank wind
65. pe of object returned depends on the intern argument passed to the rsaga geoprocessor For intern FALSE itis a numerical error code 0 success or otherwise default a character vector with the module s console output If multiple in grids are converted the result will be a vector of numerical error codes of the same length or the combination of the console outputs with c Note This function uses module 1 from the SAGA library io grid Author s Alexander Brenning R interface Olaf Conrad SAGA module See Also rsaga esri wrapper for an efficient way of applying RSAGA to ESRI ASCII binary grids rsaga env rsaga esri wrapper Use RSAGA functions for ESRI grids Description This wrapper converts input grid files provided in ESRI binary flt or ASCII asc formats to SAGA s version 2 grid format calls the RSAGA geoprocessing function and converts the output grids back to the ESRI grid format Conversion can also be limited to either input or output grids Usage rsaga esri wrapper fun in esri TRUE out esri TRUE env rsaga env esri workspace env workspace format ascii georef corner prec 5 sri extension condensed res TRUE clean up TRUE intern TRUE 30 Arguments fun in esri out esri env rsaga esri wrapper function one of the RSAGA geoprocessing functions suchas rsaga close gaps or rsaga hillshade etc logical are input gri
66. ports grid data from various file formats using the Geospatial Data Abstraction Library GDAL by Frank Warmerdam More information is available athttp www gdal org If in grid has more than one band e g RGB GEOTIFF then output grids with file names of the form n grid_01 sgrd in grid_02 sgrd etc are written one for each band The following raster formats are currently supported VRTVirtual Raster GTiffGeoTIFF NITFNational Imagery Transmission Format HFAErdas Imagine Images img SAR CEOSCEOS SAR Image CEOSCEOS Image ELASELAS AIGArc Info Binary Grid AAIGridArc Info ASCII Grid SDTSSDTS Raster DTEDDTED Elevation Raster PNGPortable Network Graphics JPEGJPEG JFIF MEMIn Memory Raster JDEMJapanese DEM mem GIFGraphics Interchange Format gif ESATEnvisat Image Format BSBMaptech BSB Nautical Charts XPMX11 PixMap Format BMPMS Windows Device Independent Bitmap PCIDSKPCIDSK Database File PNMPortable Pixmap Format netpbm rsaga insolation 47 DOQIUSGS DOQ Old Style DOQ2USGS DOQ New Style ENVIENVI hdr Labelled EHdrESRI hdr Labelled PAuxPCI aux Labelled MFFAtlantis MFF Raster MFF2Atlantis MFF2 HKV Raster FujiBASFuji BAS Scanner Image GSCGSC Geogrid FASTEOSAT FAST Format BTVTP bt Binary Terrain 1 3 Format LIBNOAA Polar Orbiter Level 1b Data Set FITFIT Image USGSDEMUSGS Optional ASCII DEM GXFGeoSoft Grid Exchange Format Author s Alexander Brenning R interface Olaf Conrad Andre Rin
67. preproc method deepen End Not run rsaga solar radiation Potential incoming solar radiation Description This function calculates the potential incoming solar radiation in an area either using a lumped atmospheric transmittance model or estimating it based on water and dust content Usage rsaga solar radiation in dem out grid out duration latitude unit c kWh m2 J m2 solconst 1367 method c lumped components transmittance 70 pressure 1013 water content 1 68 dust 100 time range c 0 24 time step 1 days list day 21 month day step 5 Arguments in dem name of input digital elevation model DEM grid in SAGA grid format default extension sgrd out grid output grid file for potential incoming solar radiation sums out duration Optional output grid file for duration of insolation latitude Geographical latitude in degree North negative values indicate southern hemi sphere unit unit of the out grid output kWh m2 default or J m2 solconst solar constant defaults to 1367 W m2 method specifies how the atmospheric components should be accounted for either based on a lumped atmospheric transmittance as specified by argument transmittance lumped or numeric code 0 default or by calculating the components cor responding to water and dust component s code 1 transmittance transmittance of the atmosphere in percent usually between 60 humid are
68. r each pixel the longitude in degree Optional output grid file for direct insolation Optional output grid file for diffuse insolation Optional output grid file for total insolation i e the sum of direct and diffuse insolation logical project radiation onto a horizontal surface default FALSE i e use the actual inclined surface as a reference area solar constant in Joule default 8 164 J cm2 min 21360 7 kWh m2 the more commonly used solar constant of 1367 kWh m2 corresponds to 8 202 J cm2 min height of atmosphere in m default 12000m pressure if no water vapour grid is given this argument specifies a constant water vapour pressure that is uniform in space in mbar default 10 mbar type of time period moment equivalent 0 for a single instant day or 1 fora single day range of days or2 or same moment range of days or 3 for the same moment in a range of days default moment time resolution in hours for discretization within a day time resolution in days for a range of days numeric vector of length 2 specifying the first and last day of a range of days for types 2 and 3 iftype moment or same moment range of days moment spec ifies the time of the day hour between 0 and 24 for which the insolation is to be calculated ifnoin latitude grid is given this will specify a fixed geographical latitude for the entire grid should planetary bending be modeled default FALSI Lj p
69. racter or numeric algorithm see References Maximum Slope Travis et al 1975 maxslope or 0 Max Triangle Slope Tarboton 1997 maxtriangleslope or 1 Least Squares Fit Plane Costa Cabral and Burgess 1996 1 et al 1985 pol and Beran 1982 Lsqfitplane or 2 Fit 2nd Degree Polynomial Bauer Ly2bauer or 3 Fit 2nd Degree Polynomial Heerdegen poly2heerdegen or 4 default Fit 2nd Degree Poly nomial Zevenbergen and Thorne 1987 poly2zevenbergen or 5 Fit 3rd Degree Polynomial Haralick 1983 poly3haralick or 6 further arguments to rsaga geoprocessor 52 Value rsaga local morphometry The type of object returned depends on the intern argument passed to the xsaga geoprocessor For intern FALSI E it is a numerical error code 0 success or otherwise default a character vector with the module s console output Note This function uses module 0 from the SAGA library ta_morphometry Author s Alexander Brenning R interface Olaf Conrad SAGA module References Maximum Slope Travis M R Elsner G H Iverson W D Johnson C G 1975 VIEWIT computation of seen PSW 11 1975 70 p areas slope and aspect for land use planning USDA F S Gen Tech Rep Berkeley California U S A Maximum Triangle Slope Tarboton D G 1997 A new method for the determination of flow directions and upslope areas in grid digital elevation models Water Ress
70. red for interpolation nmax numeric Maximum number of nearest points to be used for interpolation 54 rsaga ordinary kriging blocksize numeric block size for block kriging block kriging is applied if this parameter target Note is specified If blocksize is missing default ordinary point kriging is used list parameters identifying the target area e g the lower left corner and size of grid or name of a reference grid see rsaga target Optional arguments to be passed to rsaga geoprocessor including the env RSAGA geoprocessing environment This function uses module 4 Ordinary Kriging in SAGA library grid gridding users ofthe GUI of SAGA GIS should not be confused by the fact that the Ordinary Kriging module appears first in the GUI s module listing it is in fact module 4 The SAGA module support some other variogram models but I am not quite sure what they are doing so they and the associated additional parameters are currently not supported by this wrapper function The module s usage page also mentions a FORMULA argument but this seems to be a mistake Author s Alexander Brenning R interface Olaf Conrad SAGA module See Also rsaga inverse distance rsaga target see also krige in package gstat Examples Not run Krige attribute 0 from the points shapefile to a grid with the same extent and resolutionn as the pre existing geology grid rsaga ordinary kriging poi
71. rget grid header Arguments target character method used for defining the target grid user fit extent Only for target user defined logical if TRUE use the dimensions of an input grid supplied to the SAGA module e g to rsaga ordinary kriging The other user variables should not be provided if user fit extent TRU Gl user cellsize Only for target user defined raster resolution user x extent user y extent Only for target user defined numeric vectors of length 2 mini mum and maximum coordinates of grid cell center points user bbox Only for target user defined alternative way of specifying extent either usebbox OR user extent 2x2 matrix of the form rbind user x extent user y system nx system ny Only for target grid system number of columns and rows of the grid system xy Only for target grid system numeric vector of length 2 giving the x and y coordinates at the center of the grid s lower left cell system d Only for target grid system cellsize rsaga wetness index 63 target grid Only for target target grid character string giving the name of a SAGA grid file that specifies the extent and resolution of the target grid header Only for target header list ASCII grid header as returned e g by read ascii grid header or defined manually must at least have com ponents ncols nrows cellsize andeitherx yllcornerorx yllcenter Note This function is to be used with RSAG
72. ring prefix character string optional prefix to be added fsep character used to separate path components Author s Alexander Brenning Examples create variable name C my path my file name Rd prefix res focal function 5 focal function Local and Focal Grid Functions Description focal function cuts out square or circular moving windows from a grid matrix and applies a user defined matrix function to calculate e g a terrain attribute or filter the grid The function is suitable for large grid files as it can process them row by row local function represents the special case of a moving window of radius 1 Users can define their own functions operating on moving windows or use simple functions such as median to define filters Usage focal function in grid in factor grid out grid prefix path NULL in path path out path path fun varnames radius 0 is pixel radius TRUE na strings NA valid range c Inf Inf nodata values c out nodata value search mode c circle square digits 4 dec quiet TRUE nlines Inf mw to vector FALSE mw na rm FALSE local function gapply in grid fun varnames mw to vector TRUE mw na rm TRUI Gl Arguments in grid file name of input ASCII grid relative to in path in factor grid optional file name giving a gridded categorical variables defining zones zone boundaries are used as breaklines f
73. ry For information on the usage and arguments Value The character vector with usage information is invisibly returned Author s Alexander Brenning See Also rsaga geoprocessor rsaga env rsaga html help Examples Not run rsaga get usage io grid 1 rsaga get usage ta preprocessor 2 rsaga get usage ta morphometry 0 End Not run 40 rsaga grid calculus rsaga grid cal culus SAGA Module Grid Calculus Description Perform Arithmetic Operations on Grids Usage rsaga grid calculus in grids out grid formula saga rsaga linear coef version 2 0 4 combination in grids out grid cf digits 16 remove zeros FALSI GI remove ones TRUE Arguments in grids out grid formula saga version coef cf digits remove zeros remove ones input character vector SAGA grid files default file extension sgrd output grid file resulting from the cell by cell application of formula to the grids Existing files will be overwritten character string of formula specifying the arithmetic operation to be performed on the in grids see Details if this is a formula only the right hand side will be used character string either 2 0 4 default or 2 0 5 the command line arguments for the grid calculator module changed from SAGA GIS 2 0 4 to 2 0 5 the func tion is now able to handle both situations if using a different SAGA
74. s are provided for conveniently picking values at point locations from a grid using kriging or nearest neighbour interpolation RSAGA requires the free SAGA GIS gt 2 0 2 and its user contributed modules to be available on your computer These can be downloaded under GPL from http sourceforge net projects saga gis Please check rsaga env to make sure that RSAGA can find your local installation of SAGA Also note that SAGA GIS 2 0 5 does not seem to work well with the interface functions for interpolation methods but SAGA GIS 2 0 4 does Thanks to Olaf Conrad Andre Ringeler and all the other SAGA developers and contributors pro viding this excellent geocomputing tool Author s Alexander Brenning lt brenning uwaterloo ca gt centervalue Pick Center Value from Matrix Description Pick the value in the center of a square matrix Auxiliary function to be used by functions called by focal function Usage centervalue x Arguments x a square matrix 4 create variable name Details See for example the code of resid median Author s Alexander Brenning See Also focal function resid median Examples m matrix round runif 9 1 10 ncol 3 centervalue m create variable name Convert file name to variable name Description Convert a file name into a variable name Usage create variable name filename prefix NULL fsep Platform file sep Arguments filename character st
75. se of the matched argument or by default its name ignore case logical specifying if the matching should be case sensitive Details When choices are missing they are obtained from a default setting for the formal argument arg of the function from which match arg ext was called Matching is done using pmat ch indirectly through a call to match arg so arg may be abbre viated If arg is numeric it may take values between base and length choices base 1 base 1 will give standard 1 based R indices base 0 will give indices counted from zero as used to iden tify SAGA modules in library RSAGA Value If numeric is false and arg is a character string the function returns the unabbreviated version of the unique partial match of arg if there is one otherwise an error is signalled if several ok is false as per default When several ok is true and there is more than one match all unabbre viated versions of matches are returned If numeric is false but arg is numeric match arg ext returns name of the match correspond ing to this index counting from base i e arg base corresponds to choices 1 If numeric is true the function returns the numeric index es of the partial match of arg counted from base to length choices base 1 If arg is already numeric the function only checks whether it falls into the valid range from arg to length choices base 1 and re turns arg Author s Alexander Brenning See Also match
76. se distance weighting IDW nearest neighbors or modified quadratic shephard Usage rsaga inverse distance in shapefile out grid field power 1 maxdist 100 nmax 10 target rsaga target saga version 2 0 4 rsaga nearest neighbour in shapefile out grid field target rsaga target rsaga modified quadratic shephard in shapefile out grid field quadratic neighbors 13 weighting neighbors 19 target rsaga target 50 rsaga inverse distance Arguments in shapefile Input point shapefile default extension shp out grid Output filename for interpolated grid SAGA grid file Existing files will be overwritten field numeric number not name of attribute in the shapefile s attribute table to be interpolated the first attribute is represented by a zero power numeric 20 exponent used in inverse distance weighting usually 1 or 2 maxdist numeric maximum distance of points to be used for inverse distance interpola tion search radius nmax Maximum number of nearest points to be used for interpolation quadratic neighbors integer gt 5 weighting neighbors integer gt 3 target list parameters identifying the target area e g the lower left corner and size of grid or name of a reference grid see rsaga target saga version character string either 2 0 4 default or 2 0 5 the inverse distance module name changed from SAGA GIS 2 0 4 to 2 0 5 the rsag
77. t once FALSE is useful for processing large grids that do not fit into memory the argument is currently by default FALSE for method nearest neighbour and it currently MUST be TRUE for all other methods in these cases TRUE is the default value piecewise processing with at once FALSE is always faster than processing the whole grid at once logical provide information on the progress of grid processing on screen only relevant if at once FALSE and method nearest neighbour numeric stop after processing nlines lines of the input grid useful for testing purposes character name of a SAGA grid file default extension sgrd numeric specifying the number of digits to be used in converting a SAGA grid to an ASCII grid in pick from saga grid passed on to scan list RSAGA geoprocessing environment created by rsaga env on console a logical default FALSE indicates whether to capture the output of the com mand and show it on the R console see system rsaga geoprocessor arguments to be passed to pick from points pick from points Value 19 If cbind TRUE columns with the new interpolated variables are added to the input data frame data If cbind FALSI E a data frame only containing the new variables is returned possibly coerced to a vector if only one variable is processed Note method krige requires the gstat package pick from shapefile requires the shapefil
78. te dem sinkroute rsaga sink removal dem sinkroute dem preproc method deepen End Not run rsaga sink route Sink Drainage Route Detection Description Sink drainage route detection Usage rsaga sink route in dem out sinkroute threshold thrsheight 100 Arguments in dem input digital elevation model DEM as SAGA grid file default file extension sgrd out sinkroute output sink route grid file non sinks obtain a value of 0 sinks are assigned an integer between 0 and 8 indicating the direction to which flow from this sink should be routed threshold logical use a threshold value thrsheight numeric threshold value default 100 optional arguments to be passed to rsaga geoprocessor including the env RSAGA geoprocessing environment Value The type of object returned depends on the intern argument passed to the rsaga geoprocessor For intern FALSE itis a numerical error code 0 success or otherwise default a character vector with the module s console output Note I assume that flow directions are coded as 0 north 1 northeast 2 east 7 northwest as in rsaga fill sinks This function uses module 0 from SAGA library ta_preprocessor Author s Alexander Brenning R interface Olaf Conrad SAGA module 60 rsaga solar radiation See Also rsaga sink removal Examples Not run rsaga sink route dem sinkroute rsaga sink removal dem sinkroute dem
79. the grid header information see read ascii grid for details match arg ext 11 header optional list giving grid header information see read ascii grid for de tails varname character name to colnames names to be given to the columns corresponding to the x and y coordinates and the grid variable in the output data frame Value a data frame with three columns names are specified in the colnames argument giving the x and y coordinates and the attribute values at the locations given by the grid data Author s Alexander Brenning See Also read asciil grid pick from ascii grid Examples Not run d read ascii grid dem xyz grid to xyz d varname elevation str xyz End Not run match arg ext Extended Argument Matching Description match arg ext matches arg against a set of candidate values as specified by choices it extends mat ch arg by allowing arg to be a numeric identifier of the choices Usage match arg ext arg choices base 1 several ok FALSE numeric FALSE ignore case FALSE 12 match arg ext Arguments arg a character string or numeric value choices a character vector of candidate values base numeric value specifying the numeric index assigned to the first element of choices several ok logical specifying if arg should be allowed to have more than one element numeric logical specifying if the function should return the numerical index counting from ba
80. thor s Alexander Brenning R interface Andre Ringeler and Olaf Conrad SAGA modules rsaga local morphometry References 51 QSHEP2D Fortran routines implementing the Quadratic Shepard method for bivariate interpolation of scattered data see R J Renka ACM TOMS 14 1988 pp 149 150 Classes E2b Interpolation of scattered non gridded multivariate data See Also rsaga ordinary kriging and idw in package gstat rsaga local morphometry Local Morphometry Description Calculates local morphometric terrain attributes i e slope aspect and curvatures Usage rsaga local morphometry in dem out slope out aspect out curv out hcurv out vcurv method poly2zevenbergen rsaga slope in dem out slope method poly2zevenbergen rsaga aspect in dem out aspect method poly2zevenbergen rsaga curvature in dem out curv method poly2zevenbergen rsaga plan curvature in dem out hcurv method poly2zevenbergen rsaga profile curvature in dem out vcurv method poly2zevenbergen Arguments in dem input digital elevation model DEM as SAGA grid file default file extension Sgrd out slope optional output slope in radian out aspect optional output aspect in radian north 0 clockwise angles out curv optional output curvature out hcurv optional output horizontal curvature plan curvature out vcurv optional output vertical curvature profile curvature method cha
81. tion if available Author s Alexander Brenning See Also rsaga get usage rsaga html help rsaga geoprocessor rsaga env Examples Not run make sure that rsaga env can find saga cmd exe before running this rsaga get libraries list all modules in my favorite libraries rsaga get modules c io grid grid tools ta preprocessor ta morphometry ta lighting ta hydrology list all modules quite a few rsaga get modules interactive TRU Gl find modules that remove sink from DEMs rsaga search modules sink find modules that close gaps no data areas in grids rsaga search modules gap End Not run rsaga get usage 39 rsaga get usage Usage of SAGA command line modules Description rsaga get usage provides information on the usage of and arguments required by SAGA com mand line modules Usage rsaga get usage lib module env rsaga env show TRUI E Arguments lib name of the SAGA library module name or numeric identifier of SAGA module in library 1ib env list setting up a SAGA geoprocessing environment as created by rsaga env show logical default TRUE display usage on R console Details This funciton is intended to provide information required to use the rsaga geoprocessor and for writing your own high level interface function for SAGA modules R SAGA interfaces already exist for some SAGA modules e g rsaga hillshade rsaga local morphomet
82. tion see Details read ascii grid 21 write header logical should the header be written with the grid data default TRUE digits numeric if not missing write grid data rounded to this many digits dec character default decimal mark used in input or output file georef character specifies whether the output grid should be georeferenced by the center or corner of its lower left grid cell defaults to corner compress logical should the Rd file written by write Rd file be compressed de fault TRUE prec integer number of digits of temporary ASCII grid used for importing or export ing a SAGA grid na strings passed on to scan read sgrd write sgrd additional arguments to be passed to rsaga geoprocessor Value The read functions return either a list with components data the grid data matrix and header the grid header information see below if return header TRUE or otherwise just the grid data matrix return header FALSE The grid data matrix is a numeric matrix whose first column corrensponds to the first i e northern most row of the grid Columns run from left West to right East The header information returned by the read ascii grid header functions if return header TRUE is a list with the following components ncols Number of grid columns nrows Number of grid rows xllcorner x coordinate of the corner of the lower left grid cell yllcorner y coordinate of th
83. tput Note This function uses module 1 in the SAGA library grid filter This SAGA module had a bug under 2 0 1 which has been corrected in version 2 0 2 SAGA used to crash when this module was called Author s Alexander Brenning R interface Olaf Conrad SAGA module See Also rsaga filter simple 34 rsaga filter simple rsaga filter simple Simple Filters Description Apply a smoothing sharpening or edge filter to a SAGA grid Usage rsaga filter simple in grid out grid mode circle method c smooth sharpen edge radius Arguments in grid input SAGA grid file default file extension sgrd out grid output SAGA grid file mode character or numeric shape of moving window either square 20 or circle 1 default method character or numeric smooth 0 sharpen 1 or edge 2 radius positive integer radius of moving window optional arguments to be passed to rsaga geoprocessor including the env RSAGA geoprocessing environment Value The type of object returned depends on the intern argument passed to the rsaga geoprocessor For intern FALSE itis a numerical error code 0 success or otherwise default a character vector with the module s console output The mode argument is passed to SAGA as a MODE command line option This option used to be called SEARCH MODE under SAGA 2 0 1 so this function will cause an error under SAGA 2 0 1 Note This f
84. unction uses module 0 in the SAGA library grid filter Author s Alexander Brenning R interface Olaf Conrad SAGA module See Also rsaga filter gauss Examples Not run rsaga filter simple dem dem smooth radius 4 rsaga geoprocessor 35 rsaga geoprocessor Generic R interface for SAGA modules Description This function is the workhorse of the R SAGA interface It calls the SAGA command line tool to run SAGA modules and pass arguments Usage rsaga geoprocessor lib module NULL param list silent FALSE beep off show output on console TRUE invisible TRUE intern TRUE env rsaga env display command FALSE reduce intern TRUE Arguments lib Name of the SAGA library to be called see Details module Number gt 0 or name of the module to called within the library lib see Details param A list of named arguments to be passed to the SAGA module see Examples silent deprecated beep off is currently ignored did never really work and produced some unwanted side effects a warning is produced if beep of f is specified show output on console a logical default TRUE indicates whether to capture the output of the com mand and show it on the R console see system invisible a logical indicates whether the command window should be visible on the screen intern a logical indicates whether to make the output of the command an R object env A SAGA geoprocess
85. ve model require gam fit gam cl a s b s c data d family binomial multi focal function in grids c a p c out varnames pred fun grid predict fit fit control predict list type response control predict is passed on to grid predict which dumps its contents into the arguments for fit s predict method Model predictions are written to a file named pred asc End Not run pick from points 17 pick from points Pick Variable from Spatial Dataset Description These functions pick i e interpolate without worrying too much about theory values of a spatial variables from a data stored in a data frame a point shapefile or an ASCII or SAGA grid using nearest neighbor or kriging interpolation p ck from points is the core function that is called by the different wrappers Usage pick from points data src pick method c nearest neighbour krige set na FALSE radius 200 nmin 0 nmax 100 Sill 1 range radius nugget 0 model vgm sill nugget Sph range range nugget nugget log rep FALSE length pick X name x Y name y cbind TRUE pick from shapefile data shapefile X name x Y name y pick from ascii grid data file path varname prefix method c nearest neighbour krige nodata values c 9999 99999 at once quiet TRUE X name x Y name y nlines
86. x by replacing max by the quantile function the max function is used if prob NULL and the same result is obtained for prob 1 using the quantile function wind shelter 67 Value The function wind shelter returns the wind shelter index as described above if a numeric ma trix x is provided If it is missing it returns the character string windshelter wind shelter prep returns a list with components mask and di st Both are square matrices with 2x ceiling radius 1 columns and rows mask indicates which grid cell in the moving window is within the specified circle segment value FALSE or not TRUE dist the precomputed distances of a grid cell to the center of the moving window in map units Note The wind shelter index only makes sense if elevation is measured in the same units as the horizontal map units used for the cellsize argument i e usually meters wind shelter and wind shelter prep do notrestrict the calculation onto a circular area this is done by focal function when used in combination with that function assuming search mode circle Note that the present definition of the wind shelter index returns negative values for surfaces that are completely exposed toward the specified direction This may make sense if interpreted as a wind exposure index or it might be appropriate to set negative wind shelter values to 0 Author s Alexander Brenning References Plattner C Braun L N Brenning A

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